1887

Abstract

To identify potential selection pressures which lead to RNA sequence conservation, we examined the occurrence rates of dinucleotides in 64 singlestranded RNA virus genomes. These viruses may offer a particular insight into these pressures since their RNA-dependent RNA polymerases lack proofreading capability. This potentiates introduction of mutations into their genomes, yet unidentified selection processes conserve the genomes to a large degree. We report a strong inverse correlation between the C G content and the occurrence of the CpG dinucleotide ( = 0·71) in the RNA virus genomes, in contrast to earlier reports (Karlin ., 1994, 68, 2889–2897). We also detected significant suppression of UpA, correlating inversely with genomic U A content. These sup-pressions are coupled with over-representation of the complementary pair of dinucleotides, CpA and UpG. In addition, we highlight the fact that odds ratios for dinucleotides are not independent variables, a situation apparently not widely appreciated in the literature. This led us to view the over-representation of CpA and UpG as a consequential outcome of UpA and CpG suppression in the virus genomes. Potential factors influencing these disturbances are discussed. In addition, higher than random incidence was observed for ‘out-of-frame’ stop codons in the viral RNA genomes, with some preferences for individual codons being exhibited by certain virus groups. The UAG codon appeared more common in the M1 frame, the UGA in the 1 frame.

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1997-11-01
2022-05-26
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References

  1. Bestor T. H., Tycko B. 1996; Creation of genomic methylation patterns. Nature Genetics 12:363–367
    [Google Scholar]
  2. Beutler E., Gelbart T., Han J., Koziol J. A., Beutler B. 1989; Evolution of the genome and the genetic code: selection at the dinucleotide level by methylation and polyribonucleotide cleavage. Proceedings of the National Academy of Sciences, USA 86:192–196
    [Google Scholar]
  3. Bosma T. J., Best J. M., Corbett K. M., Banatvala J. E., Starkey W. G. 1996; Nucleotide sequence analysis of a major antigenic domain of the E1 glycoprotein of 22 rubella virus isolates. Journal ofGeneral Virology 77:2523–2530
    [Google Scholar]
  4. Breslauer K. J., Frank R., Blöcker H., Marky L. A. 1986; Predicting DNA duplex stability from the base sequence. Proceedings of the National Academy of Sciences, USA 83:3746–3750
    [Google Scholar]
  5. Burge C., Campbell A. M., Karlin S. 1992; Over- and under-representation of short oligonucleotides in DNA sequences. Proceedings of the National Academy of Sciences, USA 89:1358–1362
    [Google Scholar]
  6. Cardon L. R., Burge C., Clayton D. A., Karlin S. 1994; Pervasive CpG suppression in animal mitochondrial genomes. Proceedings of the National Academy of Sciences, USA 91:3799–3803
    [Google Scholar]
  7. Domingo E., Holland J. J. 1994; Mutation rates and rapid evolution of RNA viruses. In The Evolutionary Biology of Viruses pp. 161–184 Morse S. S. Edited by New York: Raven Press;
    [Google Scholar]
  8. Domingo E., Martinez-Salas E., Sobrino F., de la Torre J. C., Portela A., Ortin J., Lopez-Galindez C., Perez-Brena P., Villanueva N., Najera R., VanDePol S., Steinhauer D., DePolo N., Holland J. J. 1985; The quasispecies (extremely heterogeneous) nature of viral RNA genome populations: biological relevance - a review. Gene 40:1–8
    [Google Scholar]
  9. Holland J. J., Spindler K., Horodyski F., Grabau E., Nichol S., VanDePol S. 1982; Rapid evolution of RNA genomes. Science 215:1577–1585
    [Google Scholar]
  10. Jackson R. J., Kaminski A. 1995; Internal initiation of translation in eukaryotes: the picornavirus paradigm and beyond. RNA 1:985–1000
    [Google Scholar]
  11. Karlin S., Doerfler W., Cardon L. R. 1994; Why is CpG suppressed in the genomes of virtually all small eukaryotic viruses but not in those of large eukaryotic viruses?. Journal of Virology 68: 2889–2897
    [Google Scholar]
  12. Krieg A. M. 1996; Lymphocyte activation by CpG dinucleotide motifs in prokaryotic DNA. Trends in Microbiology 4:73–77
    [Google Scholar]
  13. Krieg A. M., Yi A., Matson S., Waldschmidt T. J., Bishop G. A., Teasdale R., Koretzky G. A., Klinman D. M. 1995; CpG motifs in bacterial DNA trigger direct B cell activation. Nature 374:546–549
    [Google Scholar]
  14. Li W.-H. 1987; Models for nearly neutral mutations with particular implications for nonrandom usage of synonymous codons. Journal of Molecular Evolution 24:337–345
    [Google Scholar]
  15. Rima B. K., Earle J. A. P., Baczko K., ter Meulen V., Liebert U. G., Carstens C., Carabaña J., Caballero M., Celma M. L., Fernandez-Muñoz R. 1997; Sequence divergence ofmeasles virus haemagglutinin during natural evolution and adaptation to cell culture. Journal of General Virology 78:97–106
    [Google Scholar]
  16. Serra M. J., Turner D. H. 1995; Predicting thermodynamic properties of RNA. Methods in Enzymology 259:242–261
    [Google Scholar]
  17. Sharp P. M., Matassi G. 1994; Codon usage and genetic evolution. Current Opinion in Genetics & Development 4:851–860
    [Google Scholar]
  18. Sharp P. M., Averof M., Lloyd A. T., Matassi G., Peden J. F. 1995; DNA sequence evolution: the sound of silence. Philosophical Transactions of the Royal Society of London B Biological Sciences 349:241–247
    [Google Scholar]
  19. Tinoco I. Jr Borer P. N., Dengler B., Levine M. D., Uhlenbeck O. C., Crothers D. M., Gralla J. 1973; Improved estimation of secondary structure in ribonucleic acids. Nature New Biology 246:40–41
    [Google Scholar]
  20. Wright S. 1931; Evolution in Mendelian populations. Genetics 16:97–159
    [Google Scholar]
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